The Abdo lab is interested in studying the microbiome, its interactions and function, and how it interacts with and affects its hosts’ health and is affected by its surrounding environment. This specifically includes studying the relationship between host immune system and the microbiome as it is influenced by external perturbations including vaccination, prebiotics, probiotics, antibiotics and other factors such as viral, or other, infections. This is in addition studying viral evolution and plasmid transfer and evolution as it impacts acquisition, transmission and maintenance of antimicrobial resistance. Another interest of the Abdo Lab is focused on developing and applying computational tools for processing and analysis of high throughput sequence data, and the associated metadata, in addition to developing inferential and predictive models and machine learning methods to facilitate understanding of these complex biological systems. The Abdo lab is part of the CSU Microbiome Network.
Abdo Lab Github
research project
Mucosal Immunity and the Microbiome
Challenge: Little is known about changes in the gut microbiome during vaccination, especially with an oral-probiotic vector.
Objective: Evaluate use of Lactobacillus acidophilus as a probiotic vaccine vector and the reciprocal interactions between the host’s immune response and alterations in the gut microbiome.
research project
Antimicrobial Resistance and the Microbiome
Challenge: Little is known about antimicrobial resistance reservoirs in natural environments, especially in food production. Hard to link mobile genetic elements to host microbes.
Objective: Examine the impact of both limiting and removing antibiotic use on the resistome and antimicrobial resistance evolution in poultry (food) production.
research project
Viral Ecology and Evolution
Challenge: Whole Genome Sequencing of AIV provides a faster more accurate approach and removes need for propagation in chicken eggs for AIV diagnostics.
Objective: Evaluate impact of virus isolation on virus mutation, natural selection, reassortment, and detection of co-infections.
research project
Methods for Metagenomics Classification and Modeling
Challenge: Large data sets are generated using high throughput sequencing and scalable computational tools to process and classify these data are lacking.
Objective: Develop a fast and accurate classification method for high throughput shotgun metagenomics data utilizing Low-Density Parity-Check and Naïve Bayes Classifier implemented using GPU computing.
Publications
Mosquitoes of Macha – new mosquito species records from Macha and surrounding locations in southern Zambia with photographs.
Flores IS, Nguyen VT, Bae JS, Urlaub A, Gellner R, Kading RC, Romero-Weaver AL, Simubali L, Saili K, Simulundu E, Reeves LE, Lee Y. bioRxiv [Preprint]. 2026 Jan 10:2026.01.09.698444. doi: 10.64898/2026.01.09.698444. PMID: 41542390; PMCID: PMC12803077.
Spatiotemporal patterns of airborne microbial communities in forest and grassland ecosystems.
Cornell CR, Miller AE, Nieto-Caballero M, Burns KS, Kreidenweis SM, Abdo Z, Stewart JE. mBio. 2026 Feb 11;17(2):e0305725. doi: 10.1128/mbio.03057-25. Epub 2026 Jan 16. PMID: 41543267; PMCID: PMC12892990.
Fitness Factors and Siderophores Influence the Survival of E. coli in Reused Broiler Litter.
Chung T, Oladeinde A, Woyda R, Wickramasuriya SS, Lyte JM, Liyanage R, Rothrock M, Li X, Cho S, Lawrence JP, Endale D, Strickland T, Abdo Z. . J Food Prot. 2025 Dec 10;88(12):100671. doi: 10.1016/j.jfp.2025.100671. Epub 2025 Nov 19. PMID: 41271105.
Contrasting Patterns of Raccoon (Procyon lotor) Spatial Population Genomics Throughout a Rabies Management Area in Eastern North America.
Hopken MW, Mankowski CP, Thurber C, Piaggio AJ, Nelson KM, Chipman RB, Abdo Z, Buchanan T, Massé A, Gilbert AT. Evol Appl. 2025 May 12;18(5):e70105. doi: 10.1111/eva.70105. eCollection 2025 May. PMID: 40365166
Broiler litter moisture and trace metals contribute to the persistence of Salmonella strains that harbor large plasmids carrying siderophores.
Oladeinde A, Chung T, Mou C, Rothrock MJ, Li G, Adeli A, Looft T, Woyda R, Abdo Z, Lawrence JP, Cudnik D, Zock G, Teran J, Li X. Appl Environ Microbiol. 2025 Mar 13:e0138824. doi: 10.1128/aem.01388-24. Online ahead of print. PMID: 40079597
more publications
